Skoltech research shows how a 'Swiss Army knife' protein helps phages disarm their victims



SKOLKOVO INSTITUTE OF SCIENCE AND TECHNOLOGY (SKOLTECH)


OCR, A DNA MIMIC PROTEIN OF THE WELL-STUDIED T7 PHAGE, CAN PROTECT THE VIRUS FROM BREX (FOR BACTERIOPHAGE EXCLUSION), A POORLY STUDIED SET OF BACTERIAL DEFENSE MECHANISMS UTILIZED BY, AMONG... view more  CREDIT: PAVEL ODINEV / SKOLTECH

Researchers from the Severinov Laboratory at Skoltech, along with their colleagues from Switzerland and Israel, have investigated a poorly studied bacterial BREX defense mechanism to show that it can be "turned off" by a multipurpose viral protein that successfully impersonates DNA. The paper was published in the journal Nucleic Acids Research.

In the never-ending war between bacteria and viruses that infect them, it is extremely important to know where your DNA is. To protect themselves from hostile invasion, bacteria have learned to "mark" their own genetic material by methylating it at specific sites in the genome. All "unmarked" DNA, such as that of a bacteriophage, is then recognized, cleaved and degraded by an army of endonucleases. These are called restriction modification (RM) systems. The phages, in turn, have learned to evade these RM systems by using DNA mimic proteins. A protein that chemically "looks" like DNA to the bacterial restriction complex can bind it and prevent from ever getting to actual phage DNA.

Skoltech PhD student Artem Isaev and his colleagues from Tel Aviv University and Philip Morris International R&D have shown that Ocr, a DNA mimic protein of the well-studied T7 phage, is in fact a multipurpose tool. Besides inhibition of RM type I systems, it can also protect the phage from BREX (for BacteRiophage EX?lusion), another set of bacterial defense mechanisms utilized by, among others, Escherichia coli, which T7 commonly infects.

"Five years ago, we knew about restriction modification, CRISPR and Toxin-Antitoxin abortive infection systems, but recently bioinformatics has shown us that it is just a small proportion of the real diversity of defensive strategies employed by bacteria to cope with phage infections. BREX was the first in a row of novel phage defense systems: they are found in around 1 in 10 of all microorganisms, and in bacteria they are even more widespread than CRISPR. Yet we still don't know the function of five out of six BREX genes and how they are working together to provide protection," Isaev says.

It is yet unknown whether BREX simply destroys the incoming phage DNA or somehow inhibits its replication, but almost all BREX mechanisms employ a BrxX methyltransferase, an enzyme in charge of "marking" bacterial DNA for self-recognition. The Ocr protein apparently binds to this methyltransferase and thus prevents the BREX system from both methylation of the host DNA and attacking the non-methylated phage genome.

"We have shown that Ocr interacts with methyltransferase and inhibits host DNA methylation. In theory, this can lead to an autoimmune response: as host DNA is no longer "marked" as such, BREX exclusion complexes should attack it. Yet, we do not see self-toxicity after expression of Ocr, which indicates that Ocr inhibits these exclusion complexes as well, and thus BREX methyltransferase should be involved at the active stage of defense. Ocr is already known as an inhibitor of type I RM systems, and these systems also require methytransferase for restriction complexes. There are other similarities between BREX and RM systems, and we hope that they would help us understand how BREX functions," Isaev explains.

Other DNA mimic proteins do not seem to overcome the BREX defense, so researchers intend to further investigate how exactly Ocr does its job. As bacterial defense systems mostly deal with DNA recognition and manipulation, they can become powerful tools for molecular biology and medicine. Molecular cloning is possible thanks to the discovery and description of RM systems, and CRISPR has brought about the age of genome editing. Moreover, studying the arsenals of bacteria and phages may prove useful in "recruiting" the viruses as novel antimicrobial agents in the fight against antibiotic-resistant bacteria.

"Bacteria have been combatting phages for more than a billion years, and this constant "arms race" is one of the major evolutionary forces in the microworld. Both sides have developed an enormous arsenal of strategies to fight each other, and a great diversity of molecular machines has been invented in the process. For me personally, it's just fascinating to study what else is hidden in the genome and what novel mechanism we can discover in the process," Isaev concludes.

SEE
https://plawiuk.blogspot.com/search?q=BACTERIAPHAGES

https://plawiuk.blogspot.com/search?q=PHAGES

Rice engineers: Make wastewater drinkable again

Model shows recycling could dramatically slash cities' need for fresh water resources

RICE UNIVERSITY


A SCHEMATIC REPRESENTATION OF THE HYBRID WATER SUPPLY SYSTEM DEVELOPED BY ENGINEERS AT RICE UNIVERSITY. THE RESEARCHERS SUGGEST THAT DELIVERING WATER TO CITY DWELLERS CAN BECOME FAR MORE EFFICIENT, AND... view more  CREDIT: LU LIU/RICE UNIVERSITY

HOUSTON - (April 27, 2020) - Delivering water to city dwellers can become far more efficient, according to Rice University researchers who say it should involve a healthy level of recycled wastewater.

Using Houston as a model, researchers at Rice's Brown School of Engineering have developed a plan that could reduce the need for surface water (from rivers, reservoirs or wells) by 28% by recycling wastewater to make it drinkable once again.

While the cost of energy needed for future advanced purification systems would be significant, they say the savings realized by supplementing fresh water shipped from a distance with the "direct potable reuse" of municipal wastewater would more than make up for the expense.

And the water would be better to boot.

A comprehensive model of the environmental and economic impact and benefits of such a system was developed by Rice researchers associated with the National Science Foundation-backed Nanosystems Engineering Research Center for Nanotechnology-Enabled Water Treatment (NEWT).

Rice environmental engineer Qilin Li is corresponding author and postdoctoral research Lu Liu lead author of the study that appears in Nature Sustainability.

It shows how Houston's planned reconfiguration of its current wastewater treatment system, by which it will eventually consolidate the number of treatment plants from 39 to 12, can be enhanced to "future-proof" water distribution in the city.

"All the technologies needed to treat wastewater to drinking water quality are available," Li said. "The issue is that today, they're still pretty expensive. So a very important part of the paper is to look at how cheap the technology needs to become in order for the whole thing to make sense financially and energy-wise."

Advanced water treatment happens to be a subject of intense study by scientists and engineers at the many institutions, including Rice, associated with NEWT.

"Another way to improve potable water would be to cut its travel time," she said. Water delivered by a system with many distribution points would pick up fewer chemical and biological contaminants en route. Houston, she noted, already has well-distributed wastewater treatment, and making that water drinkable would facilitate shorter travel times to homes.

The model shows there will always be a tradeoff between the acquisition of potable water, the energy required to treat it, the cost of transporting it without affecting its quality, and attempts to find a reasonable balance between those factors. The study evaluated these conflicting objectives and exhaustively examined all possibilities to find systems that strike a balance.

"Ultimately, we want to know what our next-generation water supply system should look like," Li said. "How does the scale of the system affect distribution? Should it be one gigantic, centralized water source or several smaller distributed sources?

"In that case, how many sources should there be, how big of an area should each supply and where should they be located? These are all questions we are studying," she said. "A lot of people have talked about this, but very little quantitative work has been done to show the numbers."

Li admitted Houston may not be the most representative of major municipal infrastructure systems because the city's wastewater system is already highly distributed, but its water supply system is not. The challenge of having a highly centralized water supply was demonstrated by a dramatic 96-inch water main break this February that cut off much of the city's supply.

"That was an extraordinary example, but there are many small leaks that go undetected underground that potentially allow contaminants into homes," she said.

The study only looked at direct potable reuse, which the model shows as a more economic option for established cities, but she said the best option for a new development -- that is, building a distribution system for the first time -- may be to have separate delivery of potable and nonpotable water.

"That would be prohibitive cost-wise in a place like Houston, but it would be cheaper for a new community, where wastewater effluent can be minimally treated, not quite drinkable but sufficient for irrigation or flushing toilets," Li said.

"Though maybe it would be to Houston's advantage to use detention ponds that already exist throughout the city to store stormwater and treat it for nonpotable use."

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Li is a professor of civil and environmental engineering, materials science and nanoengineering and chemical and biomolecular engineering. Co-authors of the paper are Rice alumnus Evan Lopez; Leonardo Dueñas-Osorio, an associate professor of civil and environmental engineering; Lauren Stadler, an assistant professor of civil and environmental engineering; Pedro Alvarez, the George R. Brown Professor of Civil and Environmental Engineering and a professor of chemistry and of chemical and biomolecular engineering and director of NEWT; and Yuefeng Xie, a professor of environmental engineering at Penn State University and an adjunct chair professor at Tsinghua University, China.

The National Science Foundation and the National Natural Science Foundation of China supported the research.

Read the abstract at https://www.nature.com/articles/s41893-020-0518-5

This news release can be found online at https://news.rice.edu/2020/04/27/rice-engineers-make-wastewater-drinkable-again/

Follow Rice News and Media Relations via Twitter @RiceUNews

Related materials:

Qilin Li Research Group: http://qilinli.rice.edu

Department of Civil and Environmental Engineering: https://cee.rice.edu

George R. Brown School of Engineering: https://engineering.rice.edu

Image for download:

https://news-network.rice.edu/news/files/2020/04/0427_URBAN-1-WEB.jpg

A schematic representation of the hybrid water supply system developed by engineers at Rice University. The researchers suggest that delivering water to city dwellers can become far more efficient, and that it should involve a healthy level of recycled wastewater. (Credit: Lu Liu/Rice University)

Located on a 300-acre forested campus in Houston, Rice University is consistently ranked among the nation's top 20 universities by U.S. News & World Report. Rice has highly respected schools of Architecture, Business, Continuing Studies, Engineering, Humanities, Music, Natural Sciences and Social Sciences and is home to the Baker Institute for Public Policy. With 3,962 undergraduates and 3,027 graduate students, Rice's undergraduate student-to-faculty ratio is just under 6-to-1. Its residential college system builds close-knit communities and lifelong friendships, just one reason why Rice is ranked No. 1 for lots of race/class interaction and No. 4 for quality of life by the Princeton Review. Rice is also rated as a best value among private universities by Kiplinger's Personal Finance.

Increasing green spaces in cities could prevent many premature deaths every year

A study in The Lancet Planetary Health applies a novel methodology in Philadelphia, replicable to other cities, to estimate the health impact of increasing the city's tree canopy
BARCELONA INSTITUTE FOR GLOBAL HEALTH (ISGLOBAL)

Increasing the tree canopy to 30% of land area in the city of Philadelphia (United States) could prevent over 400 premature deaths across the city every year and yield an estimated annual economic benefit of almost four billion dollars. This is the conclusion of a study published in the journal The Lancet Planetary Health, which has, for the first time, analysed the impact of increasing green spaces on premature mortality in an entire city. The project was led by the Barcelona Institute for Global Health (ISGlobal), a centre supported by "la Caixa" Foundation, and the United States Forest Service.

Research has shown that green spaces in urban settings are associated with benefits for the physical and mental health of the city's residents. A recent systematic review and meta-analysis carried out by ISGlobal, the University of Colorado and the World Health Organization (WHO) concluded that residential green spaces can protect against premature all-cause mortality. The meta-analysis, which included nine longitudinal studies involving over eight million people in seven different countries, found a significant association between an increase in green space around homes and a reduction in premature mortality.

In the new study, researchers used the dose-response function from the meta-analysis to carry out a health impact assessment and estimate the number of all-cause deaths that could be prevented if green spaces in a whole city were increased. The team studied three different possible scenarios for the city of Philadelphia for 2025. The most ambitious was based on the current goal as set by the City Council of an increase in tree coverage to 30% of land area in each of the city's neighbourhoods (current coverage is 20% for the city as a whole). The other two scenarios were less ambitious. Data on the existing canopy was obtained from aerial and satellite imagery, which allowed the researchers to measure the tree coverage by viewing the crown, leaves, branches and stems from above.

The results of the analysis showed that if Philadelphia achieves its goal of increasing tree coverage to 30% of the city by 2025, 403 premature adult deaths would be prevented each year, representing 3% of the city's annual mortality. The two more moderate scenarios were also associated with significant reductions in annual mortality: a 5% and 10% increase in tree canopy could result in an annual reduction of 271 and 376 deaths, respectively.

"Achieving this goal does not come without challenges. Large tree planting initiatives are faced with many problems, including losses from climate change, tree pests and invasive species, and urban development", explains Michelle Kondo, first author of the study.

"Although every city has its own characteristics, this study provides an example for all the cities in the world: many lives can be saved by increasing trees and greening urban environments, even at modest levels" concludes Mark Nieuwenhuijsen, the study coordinator and director of ISGlobal's Urban Planning, Environment and Health Initiative. "What's more," he adds "green spaces increase biodiversity and reduce the impact of climate change, making our cities more sustainable and more liveable".

Impact on Poor Neighbourhoods

The study also showed that neighbourhoods with a low socioeconomic level would benefit most from any increase in green spaces. "Many of the deaths prevented would be in the poorest areas of the city, even with a moderate increase in the number of trees," comments Kondo.

Philadelphia is the poorest of the ten largest cities in the United States and its mortality rate is higher than the national average. "Urban reforestation programmes are not only essential for improving public health, they are also a way to reduce health inequities and promote environmental justice," she adds.

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Reference

Kondo MC, Mueller N, Locke DH, Roman LA, Rojas-Rueda D, Schinasi L, Gascon M, Nieuwenhuijsen M, Greening Cities Can Prevent Premature Deaths: Health Impact Assessment of Philadelphia's 2015 Tree Canopy Cover Goals. The Lancet Planetary Health. April 2020.

Factors associated with disaster preparedness among US households

Association of US Households’ Disaster Preparedness With Socioeconomic Characteristics, Composition, and Region

Lucila M. Zamboni, PhD, MPP¹; Erika G. Martin, PhD, MPH²

Author Affiliations Article Information

JAMA Netw Open. 2020;3(4):e206881. doi:10.1001/jamanetworkopen.2020.6881

Key Points Español  中文 (Chinese)

Question  What characteristics are associated with resource- and action-based disaster preparedness among US households?

Findings  In this cross-sectional study using nationally representative survey data from 16 725 US households, 68.9% of households fulfilled at least half of recommended preparedness items, but households were more likely to fulfill resource- than action-based items. Fulfillment of specific resource- or action-based items differed substantially by household characteristics.

Meaning  These findings suggest that because households may treat preparedness items differently, targeted strategies are needed to promote preparedness across communities, and risk communication should emphasize the importance of both resource- and action-based preparedness.

Abstract

Importance  Since the terrorist attacks on September 11, 2001, the US government has promoted household disaster preparedness, but preparedness remains low.

Objective  To identify disparities in disaster preparedness among US households.

Design, Setting, and Participants  This cross-sectional study used data from a nationally representative sample of US households from the 2017 American Housing Survey’s topical section on preparedness to assess associations of disaster preparedness with households’ socioeconomic characteristics, composition, and region. Logistic regressions were used to assess associations of household characteristics with overall preparedness, resource- and action-based preparedness, and specific preparedness items. Data analyses were completed on March 27, 2020.

Exposures  Combined household income, head of household’s education level, race/ethnicity, marital status of head of household, head of household aged 65 years or older, presence of children or a household member with a disability, and region.

Main Outcomes and Measures  Nine actionable preparedness items, such as having an emergency carry-on kit (resource), food and water stockpiles (resource), and alternative communication plans and meeting locations (action). Items were summed for the measures of overall, resource-based, and action-based preparedness, with preparedness defined as meeting at least half of the criteria.

Results  Among 16 725 included households, 9103 household heads were men (54.4%), 11 687 were married (69.9%), and 10 749 (66.1%) had some college education or higher. In all, 1969 household heads (11.8%) were black, while 2696 were Hispanic/Latino (16.1%); 3579 household heads (21.4%) were 65 years or older. A total of 7163 households (42.8%) included children, and 3533 households (21.2%) included a person with a disability. Households were more likely to fulfill at least half of the criteria for resource-based preparedness (10 950 households [65.5%]) than for action-based preparedness (6876 households [41.1%]). Wealthy households and those with household heads aged 65 years or older were more likely to fulfill at least half of resource-based items (wealthy households: adjusted odds ratio [aOR] by logged income, 1.18 [95% CI, 1.13-1.22]; household heads age ≥65 years: aOR, 1.42 [95% CI, 1.29-1.55) but less likely to fulfill action-based items (wealthy households: aOR: 0.96 [95% CI, 0.93-0.99]; household heads age ≥65 years: aOR, 0.92 [95% CI, 0.84-0.99]). Households with black household heads were more likely to fulfill items directly related to emergencies (carry-on emergency kit: aOR, 1.26 [95% CI, 1.14-1.39]; alternative communication plan: aOR, 1.55 [95% CI, 1.39-1.72]; alternative meeting location: aOR, 1.18 [95% CI, 1.07-1.31]) but less likely to fulfill resource-based items (at least half of resource items: aOR, 0.89 [95% CI, 0.80-0.99]).

Conclusions and Relevance  These findings suggest that types of preparedness vary by household characteristics. Targeted strategies are needed to promote preparedness across communities.

TO READ THE STUDY OR DOWNLOAD PDF GO HERE

https://jamanetwork.com/journals/jamanetworkopen/fullarticle/2764814?utm_source=For_The_Media&utm_medium=referral&utm_campaign=ftm_links&utm_term=042720

Rapid evolution in fish: genomic changes within a generation

UNIVERSITY OF BASEL

THE RESEARCHERS RELEASED 3000 EXPERIMENTAL FISH INTO A NATURAL RIVER HABITAT WITHOUT STICKLEBACK, EXPOSING THEM TO NATURAL SELECTION. AFTER ONE YEAR, THE REMAINING FISH WERE RECAPTURED AND EXAMINED GENETICALLY. view more  CREDIT: UNIVERSITY OF BASEL, DARIO MOSER

Evolution is usually viewed as a slow process, with changes in traits emerging over thousands of generations only. Over the recent years, however, research has indicated that adaptation in specific traits can occur more quickly. However, very few studies outside microorganisms were able to demonstrate empirically how quickly natural selection shapes the whole genome.

A research team led by Dr. Daniel Berner at the University of Basel's Department of Environmental Sciences has now provided evidence for rapid evolution within a single generation, using threespine stickleback fish as model organism. The five-year study combined lab work, field experiments, mathematical modeling and genomic analysis.

Different habitats: lakes and rivers

In the Lake Constance area, stickleback have adapted to ecologically different habitats - lakes and rivers. To examine how quickly adaptation occurs across the genome, lake- and river-dwelling fish were crossed in the laboratory over several generations. The genomes of the two ecotypes were thus mixed, resulting in a genetically diverse experimental population.

In a second step, the researchers released thousands of these experimental fish into a natural river habitat without resident stickleback, exposing them to natural selection. After a year, the remaining fish were recaptured and examined genetically.

"The hypothesis of this experiment was that in the river habitat in which the experimental animals had to survive, genetic variants of the original river population would increase in frequency," says Berner. "However, we had no idea whether this would be measurable within a single generation."

Genomic analysis confirms hypothesis

To record potential changes in the genome, the researchers first had to identify the DNA regions most likely to be targeted by natural selection. To do so, they compared the original lake and river populations based on DNA sequence data. This revealed hundreds of regions in the genome likely important for adapting to the lake and river conditions. In precisely these regions, the experimental population's DNA sequence data from before and after the field experiment were then compared to identify changes in the frequency of genetic variants.

The result supported the hypothesis: on average, the frequency of the river variants increased by around 2.5% at the expense of the lake variants. "This difference might appear small at first glance, but is truly substantial when extrapolated over a few dozen generations," says Berner. The experiment demonstrates that evolution can occur very quickly right in front of our eyes - and not only in microorganisms. "Such rapid evolution may help some organisms to cope with the current rapid environmental changes caused by humans," Berner concludes.

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'We urgently need a renewed public debate about new breeding technologies'

Göttingen agricultural economist evaluates research results on food security
UNIVERSITY OF GÖTTINGEN

GENE-EDITING TECHNOLOGIES CAN HELP TO MAKE SMALLHOLDER FARMING IN AFRICA MORE PRODUCTIVE, ENVIRONMENTALLY-FRIENDLY, AND CLIMATE SMART view more  CREDIT: S KOPPMAIR
Plant breeding has considerably increased agricultural yields in recent decades and thus made a major contribution to combating global hunger and poverty. At the same time, however, the intensification of farming has had negative environmental effects. Increases in food production will continue to be crucial for the future because the world population and demand continue to grow. A recent study by the University of Göttingen shows that new plant breeding technologies - such as genetic engineering and gene editing - can help to increase food production whilst being more environmentally friendly. The results have been published in the journal Applied Economic Perspectives and Policy.

For the study, the agricultural economist Professor Matin Qaim from the University of Göttingen evaluated 50 years' worth of research from around the world. Since the 1960s, there has been a "Green Revolution": high-yielding varieties of wheat, rice and maize have been developed and widely cultivated, especially in Asia and Latin America. As a result, crop yields tripled, which not only increased farmers' incomes, but also improved ordinary consumers' access to food. However, the high yields were accompanied by intensive use of chemical fertilizers and pesticides. In addition, developments concentrated on a small number of cereal species, which led to a reduction in agricultural diversity.

"Cereals are cheap sources of calories, which explains why hunger has been significantly reduced in recent decades," explains Qaim. "Unfortunately, the Green Revolution was less successful in combating widespread micronutrient deficiency. This requires a more balanced diet and more diversity in agricultural production with more beans, vegetables, fruit and other locally adapted species."

New molecular breeding technologies can help modify plants to produce higher yields. In addition, plants can be bred to require less fertilizer and pesticides because they make better use of soil nutrients and are more resistant to disease, pests and extreme weather conditions. The new technologies can also speed up the breeding of new traits, enabling faster adaptation to climate change. "Even though new methods like CRISPR were only invented a few years ago, they have already been used successfully in many different crops. The methods are relatively simple and inexpensive, so even small laboratories can use them to improve local species. This is an important step towards greater diversity," says Qaim.

Genetically modified organisms (GMO) have been grown for about 25 years but remain controversial, especially in Europe. Although these varieties are classified as safe in scientific studies, there is still widespread public concern about possible health and environmental risks. To a large extent, these concerns are related to the fact that GMOs contain genes introduced from other species. "The low public acceptance has led to high regulatory hurdles that are not scientifically justified and seriously slow down the development of the technology," explains Qaim. Gene-editing methods are different because they usually do not transfer foreign genes. In principle, the targeted changes in the plant's DNA could occur naturally. "The problem is that the regulatory authorities in Europe treat plants developed using gene editing in the same way as genetically modified plants where foreign genes are introduced. This fuels public fears and prevents the further development and use of the technology in agriculture. Unfortunately, the European attitude has far-reaching implications for many poor countries, especially in Africa, where new agricultural technologies are particularly important for small farms," says Qaim. "We urgently need a different and more evidence-based public discourse about new breeding technologies, because they can make an important contribution to sustainable agriculture and food security."

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Original publication: Qaim, M. (2020). Role of new plant breeding technologies for food security and sustainable agricultural development. Applied Economic Perspectives and Policy, https://doi.org/10.1002/aepp.13044

Paper also available here: https://onlinelibrary.wiley.com/doi/full/10.1002/aepp.13044

Contact:

Professor Matin Qaim
University of Göttingen
Faculty of Agricultural Sciences - Department of Agricultural Economics and Rural Development
Platz der Göttinger Sieben 5, 37073 Göttingen, Germany
Tel: +49 (0)551 39-24806
Email: mqaim@uni-goettingen.de
http://www.uni-goettingen.de/en/42360.html

Papua New Guinea highland research redates Neolithic period


UNIVERSITY OF OTAGO

UNIVERSITY OF OTAGO PROFESSOR OF ARCHAEOLOGY PROFESSOR GLENN SUMMERHAYES WITH FIELD CREW IN PAPUA NEW GUINEA. view more  CREDIT: UNIVERSITY OF OTAGO
A new report published in Science Advances on the emergence of agriculture in highland Papua New Guinea shows advancements often associated with a later Neolithic period occurred about 1000 years' earlier than previously thought.

University of Otago Archaeology Programme Professor and report co-author Glenn Summerhayes says findings in Emergence of a Neolithic in highland New Guinea by 5000 to 4000 years ago, provide insights into when and how the highlands were first occupied; the role of economic plants in this process; the development of trade routes which led to the translocation of plants and technologies; and an associated record of landscape, environment and climate change through time.

The report details the earliest figurative stone carving and formally manufactured pestles in Oceania, dating to 5050 to 4200 years ago, which were found at a dig site in Waim. Also found were the earliest planilateral axe-adzes uncovered in New Guinea to date, and the first evidence for fibrecraft and interisland obsidian transfer from neighbouring islands over distances of at least 800km.
"The new evidence from Waim fills a critical gap in our understanding of the social changes and technological innovations that have contributed to the developing cultural diversity in New Guinea," Professor Summerhayes says.

The combination of symbolic social systems, complex technologies, and highland agricultural intensification supports an independent emergence of a Neolithic around 1000 years before the arrival of Neolithic migrants, the Lapita, from Southeast Asia. When considered together with a growing corpus of studies indicating expansion and intensification of agricultural practices, these combined cultural elements represent the development of a regionally distinct Neolithic.
The research establishes dating for other finds at the site, including a fire lighting tool, postholes, and a fibrecraft tool with ochre, possibly used for colouring string fibre.

The report suggests increased population pressure on the uneven distribution of natural resources likely drove this process, which is further inferred by language and genetic divergence.

The project arose out of an Australian Research Council Grant awarded to Dr Judith Field (University of New South Wales) and Professor Summerhayes.

"Former Otago postgraduate student Dr Ben Shaw was employed as postdoctoral fellow to do the "leg work in the field" and Dr Anne Ford (Otago Archaeology Programme) contributed to understandings of the stone tool technologies. As it worked out many of these rich discoveries were made by Dr Shaw. It was one of the best appointments Dr Field and I have ever made. I am proud of our Otago graduates who are some of the best in the world."

Professor Summerhayes and his team had previously completed a Marsden funded project in the Ivane Valley of Papua, establishing the beginning of human occupation at 50,000 years ago. The results of this work were published in Science in 2010.

"This project is a follow-on where we wanted to construct a chronology of human presence in the Simbai/Kaironk Valley of Papua New Guinea by systematic archaeological survey with subsequent excavation and analysis of a select number of sites.

"This work tracks long-term patterns of settlement history, resource use and trade, and establishes an environmental context for these developments by compiling vegetation histories, with particular attention paid to fire histories, indicators of landscape disturbance and markers of climate variability. This will add to understandings of peoples' impact on the environment."

Professor Summerhayes received a Marsden grant in late 2019 for his project "Crossing the divide from Asia to the Pacific: Understanding Austronesian colonisation gateways into the Pacific". This will involve work in the Ramu Valley, which was once part of an inland sea, and will tie in the developments of Highland New Guinea, with the movements of Austronesian speakers into the Pacific.

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For further information contact
Professor Glenn Summerhayes
University of Otago, Department of Archaeology
Email: glenn.summerhayes@otago.ac.nz

Milk pioneers: East African herders consumed milk 5,000 years ago


WASHINGTON UNIVERSITY IN ST. LOUIS

A MODERN DAY KENYAN COLLECTS FRESH COW'S MILK IN A GOURD. 

view more  CREDIT: OLIVER RUDD
When you pour a bowl of cereal, you probably aren't considering how humans came to enjoy milk in the first place. But animal milk was essential to east African herders at least 5,000 years ago, according to a new study that uncovers the consumption habits in what is now Kenya and Tanzania -- and sheds a light on human evolution.

Katherine M. Grillo, assistant professor of anthropology at the University of Florida and a 2012 PhD graduate of Washington University in St. Louis, teamed up with researchers, including Washington University's Fiona Marshall, the James W. and Jean L. Davis Professor in Arts & Sciences, for the study published this week in the Proceedings of the National Academy of Sciences. Julie Dunne at the University of Bristol in the United Kingdom is co-first author on the paper with Grillo.

After excavating pottery at sites throughout east Africa, team members analyzed organic lipid residues left in the pottery and were able to see evidence of milk, meat and plant processing.

"(This is) the first direct evidence we've ever had for milk or plant processing by ancient pastoralist societies in eastern Africa," Grillo said.

"The milk traces in ancient pots confirms the story that bones have been telling us about how pastoralists lived in eastern Africa 5,000 to 3,000 years ago -- an area still famous for cattle herding and the historic way of life of people such as Maasai and Turkana," Marshall said.

Marshall continued: "Most people don't think about the fact that we are not really designed to drink milk as adults -- most mammals can't. People who had mutations that allowed them to digest fresh milk survived better, we think, among herders in Africa. But there's a lot we don't know about how, where and when this happened.

"It's important because we still rely on our genetics to be able to drink fresh cow's milk once we are adults."

This research shows, for the first time, that herders who specialized in cattle -- as opposed to hunting the abundant wildlife of the Mara Serengeti -- were certainly drinking milk.

"One of the reasons pastoralism has been so successful around the world is that humans have developed lactase persistence -- the ability to digest milk due to the presence of specific alleles," Grillo said.

Notably, in east Africa there are distinctive genetic bases for lactase persistence that are different from other parts of the world. Geneticists believed that this ability to digest milk in northeast Africa evolved around 5,000 years ago, but archaeologists knew little about the archaeological contexts in which that evolution took place.

The development of pastoralism in Africa is unique as well, where herding societies developed in areas that often can't support agriculture.

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Molecular & isotopic evidence of milk, meat & plants in prehistoric food systems
COOKBOOK COMING SOON
UNIVERSITY OF BRISTOL


IMAGE: EXAMPLES OF POTSHERDS ANALYSED view more
CREDIT: KATE GRILLO

A team of scientists, led by the University of Bristol, with colleagues from the University of Florida, provide the first evidence for diet and subsistence practices of ancient East African pastoralists.

The development of pastoralism is known to have transformed human diets and societies in grasslands worldwide. Cattle-herding has been (and still is) the dominant way of life across the vast East African grasslands for thousands of years.

This is indicated by numerous large and highly fragmentary animal bone assemblages found at archaeological sites across the region, which demonstrate the importance of cattle, sheep and goat to these ancient people.

Today, people in these areas, such as the Maasai and Samburu of Kenya, live off milk and milk products (and sometimes blood) from their animals, gaining 60 - 90 percent of their calories from milk.

Milk is crucial to these herders and milk shortages during droughts or dry seasons increase vulnerabilities to malnutrition, and result in increased consumption of meat and marrow nutrients.

Yet we do not have any direct evidence for how long people in East Africa have been milking their cattle, how herders prepared their food or what else their diet may have consisted of.

Significantly though, we do know they have developed the C-14010 lactase persistence allele, which must have resulted from consumption of whole milk or lactose-containing milk products. This suggests there must be a long history of reliance on milk products in the area.

To address this question, the researchers examined ancient potsherds from four sites in Kenya and Tanzania, covering a 4000-year timeframe (c 5000 to 1200 BP), known as the Pastoral Neolithic, using a combined chemical and isotopic approach to identify and quantify the food residues found within the vessels. This involves extracting and identifying the fatty acids, residues of animal fats absorbed into the pot wall during cooking.

The findings, published today in the journal PNAS, showed that by far the majority of the shards yielded evidence for ruminant (cattle, sheep or goat) meat, bones, marrow and fat processing, and some cooking of plants, probably in the form of stews.

This is entirely consistent with the animal bone assemblages from the sites sampled. Across this entire time frame, potsherds preserving milk residues were present at low frequencies, but this is very similar to modern pastoralist groups, such as the heavily milk-reliant Samburu, who cook meat and bones in ceramic pots but milk their cattle into gourds and wooden bowls, which rarely preserve at archaeological sites.

In the broader sense, this work provides insights into the long-term development of pastoralist foodways in east Africa and the evolution of milk-centred husbandry systems. The time frame of the findings of at least minor levels of milk processing provides a relatively long period (around 4,000 years) in which selection for the C-14010 lactase persistence allele may have occurred within multiple groups in eastern Africa, which supports genetic estimates. Future work will expand to studies of other sites within the region.

Dr Julie Dunne, from the University of Bristol's School of Chemistry, who led the study, said: "How exciting it is to be able to use chemical techniques to extract thousands of year-old foodstuffs from pots to find out what these early East African herders were cooking.

"This work shows the reliance of modern-day herders, managing vast herds of cattle, on meat and milk-based products, has a very long history in the region."

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Neolithic genomes from modern-day Switzerland indicate parallel ancient societies

Genetic analysis of 96 ancient individuals traces the arrival and demographic structure of peoples with Steppe-related ancestry into late Neolithic, early Bronze Age Switzerland
MAX PLANCK INSTITUTE FOR THE SCIENCE OF HUMAN HISTORY


IMAGE: TOP VIEW OF THE DOLMEN OF OBERBIPP, ONE OF THE LARGEST BURIAL SITES IN THE STUDY. IN THIS STUDY, RESEARCHERS ANALYZE 96 ANCIENT GENOMES TO TRACE THE ARRIVAL AND... view more  CREDIT: URS DARDEL, ARCHÄOLOGISCHER DIENST DES KANTON BERN (SWITZERLAND)

Genetic research throughout Europe shows evidence of drastic population changes near the end of the Neolithic period, as shown by the arrival of ancestry related to pastoralists from the Pontic-Caspian steppe. But the timing of this change and the arrival and mixture process of these peoples, particularly in Central Europe, is little understood. In a new study published in Nature Communications, researchers analyze 96 ancient genomes, providing new insights into the ancestry of modern Europeans.

Scientists sequence almost one hundred ancient genomes from Switzerland

With Neolithic settlements found everywhere from lake shore and bog environments to inner alpine valleys and high mountain passes, Switzerland's rich archeological record makes it a prime location for studies of population history in Central Europe. Towards the end of the Neolithic period, the emergence of archaeological finds from Corded Ware Complex cultural groups (CWC) coincides with the arrival of new ancestry components from the Pontic-Caspian steppe, but exactly when these new peoples arrived and how they mixed with indigenous Europeans remains unclear.

To find out, an international team led by researchers from the University of Tübingen, the University of Bern and the Max Planck Institute for the Science of Human History (MPI-SHH) sequenced the genomes of 96 individuals from 13 Neolithic and early Bronze Age sites in Switzerland, southern Germany and the Alsace region of France. They detect the arrival of this new ancestry as early as 2800 BCE, and suggest that genetic dispersal was a complex process, involving the gradual mixture of parallel, highly genetically structured societies. The researchers also identified one of the oldest known Europeans that was lactose tolerant, dating to roughly 2100 BCE.

Slow genetic turnover indicates highly structured societies

"Remarkably, we identified several female individuals without any detectable steppe-related ancestry up to 1000 years after this ancestry arrives in the region," says lead author Anja Furtwängler of the University of Tübingen's Institute for Archeological Sciences. Evidence from genetic analysis and stable isotopes suggest a patrilocal society, in which males stayed local to where they were born and females came from distant families that did not carry steppe ancestry.

These results show that CWC was a relatively homogenous population that occupied large parts of Central Europe in the early Bronze Age, but they also show that populations without steppe-related ancestry existed parallel to the CWC cultural groups for hundreds of years.

"Since the parents of the mobile females in our study couldn't have had steppe-related ancestry either, it remains to be shown where in Central Europe such populations were present, possibly in the Alpine mountain valleys that were less connected to the lower lands" says Johannes Krause, director of the Department of Archaeogenetics at MPI-SHH and senior author of the study. The researchers hope that further studies of this kind will help to illuminate the cultural interactions that precipitated the transition from the Neolithic to the Early Bronze age in Central Europe.

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